2ZUR | pdb_00002zur

Crystal Structure of Rh(nbd)/apo-Fr

• PDB DOI: https://doi.org/10.2210/pdb2ZUR/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Equus caballus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-10-28 Released: 2009-06-02 
• Deposition Author(s): Abe, S., Hirata, K., Ueno, T., Shimizu, N., Yamamoto, M., Takata, M., Watanabe, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.196 (Depositor), 0.195 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.176 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Starting Model: experimental

Literature

Polymerization of phenylacetylene by rhodium complexes within a discrete space of apo-ferritin

Abe, S., Hirata, K., Ueno, T., Morino, K., Shimizu, N., Yamamoto, M., Takata, M., Yashima, E., Watanabe, Y.

(2009) J Am Chem Soc 131: 6958-6960

• PubMed: 19453195 
• DOI: https://doi.org/10.1021/ja901234j
• Primary Citation Related Structures: 
  2ZUR


• PubMed Abstract: 
  

  Polymerization reactions of phenylacetylene derivatives are promoted by rhodium complexes within the discrete space of apo-ferritin in aqueous media. The catalytic reaction provides polymers with restricted molecular weight and a narrow molecular weight distribution. These results suggest that protein nanocages have potential for use as various reaction spaces through immobilization of metal catalysts on the interior surfaces of the protein cages.

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Organizational Affiliation: 
• Institute for Integrated Cell-Material Sciences, Funai Center, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.

Biological Assembly 1  

Global Symmetry: Octahedral - O  (Explore in 3D)
Global Stoichiometry: Homo 24-mer - A24 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 21.52 kDa 
• Atom Count: 1,710 
• Modeled Residue Count: 173 
• Deposited Residue Count: 174 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferritin light chain	A [auth X]	174	Equus caballus	Mutation(s): 0  Gene Names: FTL
UniProt
Find proteins for P02791 (Equus caballus) Explore P02791  Go to UniProtKB:  P02791

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CD	B [auth X], C [auth X], D [auth X], E [auth X], F [auth X]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
RH	I [auth X], J [auth X]	Rhodium Rh OBDSITLACDGNMC-UHFFFAOYSA-N
SO4	G [auth X], H [auth X]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	K [auth X], L [auth X], M [auth X], N [auth X], O [auth X], P [auth X], Q [auth X], R [auth X]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
C4R	A [auth X]	L-PEPTIDE LINKING	C10 H14 N O2 Rh S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.196 (Depositor), 0.195 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.176 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: F 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 181.276	α = 90
b = 181.276	β = 90
c = 181.276	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-06-02 
Deposition Author(s): Abe, S., Hirata, K., Ueno, T., Shimizu, N., Yamamoto, M., Takata, M., Watanabe, Y.

Revision History  

• Version 1.0: 2009-06-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-11-15
  Changes: Data collection
• Version 1.4: 2024-10-23
  Changes: Structure summary